Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “hypervariable regions”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,459 records · Page 81Linked to original sources
PubMed1998

[Paleogenetic analysis of the skeletons from the sepulchral cave of Elzarreko Karbia (Bronze Age, Basque Country)].

Through paleogenetic studies we have characterised the sampling of a sepulchral cave named Elzarreko Karbia, in the Basque Country (France). Four people had been buried in this cave in the Ancient Bronze Age, three men, including an adolescent, and a woman, dating from 3,700 BP. In addition to a confirmation of the anatomical sex determination through amelogenin first intron amplification, we obtained a mitochondrial second hypervariable region (HVR II) sequence for each individual, and thus, we excluded maternal relationship between some of the skeletons.

Adolescent↗
PubMed2002

Possible role of mtDNA mutations in sudden infant death.

Variation in hypervariable region I (HVR-I) and mutations in coding areas of mtDNA were studied in 257 patients of sudden infant death caused by infections, sudden infant death syndrome (SIDS), and borderline SIDS and in a control group of 102 living infants. Nine different point mutations were detected in the coding areas investigated: T3290C, T3308C, T3308G (three patients), A9299G (two patients), G9300A (two patients), T10034C (nine patients), A10042T, C10043T, and A10044G. An association was found between a high number of HVR-I substitutions and potentially pathogenic mtDNA point mutations in coding areas (P = 0.024, odds ratio = 1.3). The mean number of substitutions in HVR-I was 3.28 in the infectious death group, 2.63 in the borderline SIDS group, 2.58 in the SIDS group, and 2.02 in the control group (P = 0.005). In coding areas, 11.1% of the infectious death patients had a mutation, and the same was true for 9.8% of the borderline SIDS patients, 5.6% of the SIDS patients, and 2.9% of the control subjects (P = 0.21). The results indicate that increased levels of HVR-I substitutions may be an indicator of mtDNA instability. Furthermore, mtDNA mutations may play a role in some patients with sudden unexpected infant death that was unexplained or thought to be caused by infection.

Complementarity Determining Regions↗
PubMed1995

Identification of Mycobacterium tuberculosis complex, Mycobacterium avium and Mycobacterium intracellulare by selective nested polymerase chain reaction.

A nested polymerase chain reaction (PCR) procedure was devised for identification of mycobacteria. The outer reaction exploiting genus-specific sequences on the 16S rRNA gene was able to amplify specifically strains of the genus Mycobacterium. The identification of Mycobacterium tuberculosis complex, Mycobacterium avium and Mycobacterium intracellulare was accomplished by selective reamplification of the outer PCR product in three distinct inner amplifications exploiting species-specific primers mapping to a hypervariable region of mycobacterial 16S rRNA. Detection of mycobacteria, other than those for which species-specific primers were used, was accomplished by adding a supplementary genus-specific upper primer to one of the inner reactions. Specificity of amplification was confirmed for clinical isolates and reference strains of different mycobacterial species with the exception of a M. intracellulare type 7 strain which was recognized as M. avium. The amplification protocol presented thus provides a reliable and cost-effective way for identification of clinically relevant mycobacteria.

Base Sequence↗
PubMed1995

Study of anti-idiotype antibodies to the monoclonal antibody HGT3a and its relation to the 38 kDa antigen of Mycobacterium tuberculosis.

The hypervariable regions of the immunoglobulins which function as the antigen binding sites are capable of provoking an antibody response and are referred to as anti-idiotypic antibodies. Antisera were raised in rabbits against the idiotypes of a mouse monoclonal antibody HGT3a which binds only to the 38 kDa antigen of the M. tuberculosis complex group of organisms. Idiotype specificity in these antisera was determined by dot ELISA, Western blot and solid phase inhibition assays. In vivo administration of this rabbit anti-idiotypic antibody to Swiss mice evoked an anti-anti-idiotypic antibody response, further confirming the internal antigen mimicry by the anti-idiotypic antibodies of the 38 kDa antigenic epitope and its potential use as a surrogate antigen. Antibody response to the anti-idiotypic antibodies in the sera of patients with pulmonary tuberculosis showed significant correlation with the antibody response to the 38 kDa antigen studied in the same clinical samples indicating a close similarity of the 38 kDa antigen of M. tuberculosis and the rabbit anti-idiotypic antibody produced against MoAb HGT3a.

Animals↗
PubMed1991

Genetics of diabetes. Genes and environment.

Many other autoimmune and chronic diseases exhibit marked geographic variation in incidence, which has been attributed to environmental differences across populations (Hutt and Burkitt, 1986). The results of our international IDDM research have provided evidence for the importance of large genetic variations in the frequency of HLA susceptibility genes between racial groups and countries. One may speculate that differences in the prevalence of susceptibility genes for other chronic diseases exist and significantly contribute to the geographic patterns of incidence of these disorders. Other autoimmune diseases are known to have epidemiological features similar to those described for IDDM. Although they are also characterized by an underlying HLA-related susceptibility, environmental factors are known to play an important aetiological role (Tiwari and Terasaki, 1985). DNA polymorphisms of the DR, DQ and DP locus antigens are associated with various autoimmune diseases (Todd et al, 1988; Thorsby et al, 1989). These molecular variations are similar to those described for IDDM, in that they are typically related to the hypervariable regions of the molecule and, thus, affect the peptide binding ability of the antigen. Based on the evidence for IDDM, population differences in the frequency of other HLA susceptibility genes are likely to be major determinants of the geographic distribution of diseases such as rheumatoid arthritis and multiple sclerosis. The epidemiological approach outlined in this review is, thus, applicable to other autoimmune diseases and will significantly contribute to our knowledge of the aetiology of these disorders. The emerging field of molecular epidemiology represents a new research approach which will lead to a better understanding of the relationships between specific risk factors and the aetiology of chronic diseases within populations and across the world.

Diabetes Mellitus, Type 1↗
PubMed1997

Restriction fragment length polymorphism analysis reveals different allele frequency and a linkage disequilibrium at locus D1S94 in neuroblastoma patients.

Deletion of chromosome 1p and MYCN amplification have been reported as frequent abnormalities in human neuroblastoma. We studied loss of heterozygosity (LOH) in 50 (48 informative) Italian neuroblastoma patients by restriction fragment length polymorphisms (RFLPs) analysis using anonymous and hypervariable region (HVR) sequences. Twelve cases (25%) showed LOH at one or more loci. Locus D1S94 was the most frequently involved in LOH events (8/12) of deleted cases (66.6%). MYCN amplification was observed in 20% of patients which showed a significantly lower event-free survival probability (EFSp) (P = 0.004). We also studied the allelic distribution in the constitutional DNA of neuroblastoma patients (n = 44) and a matched group of healthy Italian subjects (n = 79) for loci D1S112 and D1S94. A significantly (P = 0.01) different allele frequency was detected for the two groups at locus D1S94, but not at D1S112. Moreover, the neuroblastoma population did not confirm the Hardy-Weinberg expectations at the former locus. This observation suggests the existence of an allelotype associated with neuroblastoma susceptibility.

Alleles↗
PubMed2000

NMR structure of an anti-gp120 antibody complex with a V3 peptide reveals a surface important for co-receptor binding.

BACKGROUND: The protein 0.5beta is a potent strain-specific human immunodeficiency virus type 1 (HIV-1) neutralizing antibody raised against the entire envelope glycoprotein (gp120) of the HIV-1(IIIB) strain. The epitope recognized by 0.5beta is located within the third hypervariable region (V3) of gp120. Recently, several HIV-1 V3 residues involved in co-receptor utilization and selection were identified. RESULTS: Virtually complete sidechain assignment of the variable fragment (Fv) of 0.5beta in complex with the V3(IIIB) peptide P1053 (RKSIRIQRGPGRAFVTIG, in single-letter amino acid code) was accomplished and the combining site structure of 0.5beta Fv complexed with P1053 was solved using multidimensional nuclear magnetic resonance (NMR). Five of the six complementarity determining regions (CDRs) of the antibody adopt standard canonical conformations, whereas CDR3 of the heavy chain assumes an unexpected fold. The epitope recognized by 0.5beta encompasses 14 of the 18 P1053 residues. The bound peptide assumes a beta-hairpin conformation with a QRGPGR loop located at the very center of the binding pocket. The Fv and peptide surface areas buried upon binding are 601 A and 743 A(2), respectively, in the 0.5beta Fv-P1053 mean structure. The surface of P1053 interacting with the antibody is more extensive and the V3 peptide orientation in the binding site is significantly different compared with those derived from the crystal structures of a V3 peptide of the HIV-1 MN strain (V3(MN)) complexed to three different anti-peptide antibodies. CONCLUSIONS: The surface of P1053 that is in contact with the anti-protein antibody 0.5beta is likely to correspond to a solvent-exposed region in the native gp120 molecule. Some residues of this region of gp120 are involved in co-receptor binding, and in discrimination between different chemokine receptors utilized by the protein. Several highly variable residues in the V3 loop limit the specificity of the 0.5beta antibody, helping the virus to escape from the immune system. The highly conserved GPG sequence might have a role in maintaining the beta-hairpin conformation of the V3 loop despite insertions, deletions and mutations in the flanking regions.

Amino Acid Sequence↗
PubMed2004

Evolution and phylogenetic utility of CAD (rudimentary) among Mesozoic-aged Eremoneuran Diptera (Insecta).

We sequenced nearly the entire carbomoylphosphate synthase (CPS) domain of CAD, or rudimentary, (ca. 4 kb) from 29 species of flies representing all major clades within Eremoneura, or higher flies, and several orthorrhaphous brachyceran outgroups. We compared these sequences with orthologs from Anopheles gambiae and Drosophila melanogaster to assess structure, compositional bias, and phylogenetic utility. CAD is large (6.6+ kb), complex (comprised of three major and myriad minor functional domains) and relatively free of introns, extreme nucleotide bias (except third codon positions), and large hypervariable regions. The CPS domain possesses moderate levels of nonsynonymous divergence among taxa of intermediate evolutionary age and conveys considerable phylogenetic signal. Phylogenetic analysis of CPS sequences under varying methods and assumptions resulted in well-resolved, strongly supported trees concordant with many traditional ideas about higher dipteran phylogeny and with prior inferences from 28S rDNA. The most robustly supported major eremoneuran clades were Cyclorrhapha, Platypezoidea, Eumuscomorpha, Empidoidea, Atelestidae, Empidoidea exclusive of Atelestidae, Hybotidae s.l., Microphoridae+Dolichopodidae, and Empididae s. str. Because CAD is ubiquitous, apparently single copy (at least within holometabolous insects), readily obtained from several insect orders using primers described herein, and exhibits considerable phylogenetic utility, it should have wide applicability in insect molecular systematics.

Animals↗
PubMed2000

[Discovery of a chronic HVC infection without seroconversion in a blood donor in France during 28 months].

The HCV-RNA screening technique developed by the French Fractionation and Biotechnology Laboratory singled out in March 1998 a case of positive HCV-RNA viremia in a blood donor without any anti-HCV antibody. That donor was a 46-year-old woman who had made 54 donations of blood products from 1988 to 1997. She had no history of blood transfusion, no history of hepatitis and no life-style risk factor. Clinical examination was normal. Liver tests (serum alanine amino transferases, gamma glutamyl transpeptidase , alkaline phosphatase, bilirubin , prothrombin and albumin) were normal. Total blood count was normal. Lymphocyte count was normal as well as in vitro functional analysis of lymphocytes (stimulation with different antigens). All screening HCV Elisa tests and immunoblot System available on the French market were unable to detect anti-HCV antibodies. Quantification of serum HCV-RNA (Amplicor Monitor Roche) showed 294,000 copies/mL and HCV genotype 1b determination was performed using Innolipa assay. Further examination of the HCV genotype by direct sequencing of the PCR product showed a classical 1b genotype sequence. The hemovigilance inquiry identified 25 labile products distributed since 1988. Analyzing the records of the recipients that have so far been traced and identified revealed three periods: 1997 to 1995: three recipients were found to be positive for anti-HCV antibodies; two are now cured of hepatitis C. In one recipient, direct sequencing after specific PCR of the hypervariable region coding for the envelope domain showed 100% homology with the donor; 1993 to 1990: four recipients were identified and traced without contamination; in 1988: three of four blood product recipients were anti-HCV negative without HCV-RNA viremia. The forth carried anti-HCV antibodies and genotype 1b HCV-RNA but had a history of multiple surgery. Alter et al. [4] and Bush et al. [5] have previously suggested the possibility of a chronic, immunologically silent state of infection. The case described herein, is the first evidence for this hypothesis. Indeed, the donor has not yet seroconverted 28 months after viremia was discovered. This blood donor was identified by HCV-RNA screening of plasma products. The identification of the same sequence in a recipient of blood from this donor clearly establishes the transmission of the virus by transfusion. The prevalence of such cases of infectious silent chronic HCV carriers has to be determined and the mechanisms responsible for the absence of antibody production need to be clarified.

Amino Acid Sequence↗
PubMed2003

Variability of mitochondrial DNA in a population sample from Iceland.

Over the past decade investigations of human mitochondrial DNA (mtDNA) have considerably contributed to our knowledge about human evolution and migration. The genome of the Icelandic population is of special interest since Iceland has been genetically isolated for centuries. The sequence of the hypervariable regions HVS-I and HVS-II of the mtDNA control region was generated for 100 Icelandic individuals. A total of 75 different mtDNA sequences were observed, of which 19 sequences were shared by more than one individual, 16 sequences were shared by two individuals and two sequences were shared by three individuals; the most frequent haplotype (16129 A, 16239 T, 00263 G and 00315.1 C) was found six times. Both the genetic diversity (0.9925+/-0.0031) and the average number of pairwise nucleotide differences (7.371) were comparable with most of the other European populations. However, we found a smaller number of distinct mitochondrial lineages, suggesting that founder effects and genetic drift may have exerted a visible influence on the Icelandic genetic diversity. We compared these data with 1400 other European sequences from the D-Loop-BASE database. The paper discusses the evolutionary relationship between Icelandic and Central European mtDNA under due consideration of the historical context. Finally, our study has been aimed at increasing the number of mtDNA sequences available throughout the world and contributing to human genome investigations.

DNA Fingerprinting↗
PubMed2003

Sequence polymorphism of mitochondrial DNA in Japanese individuals from Gifu Prefecture.

Sequence polymorphisms of the hypervariable region HV1 in mitochondrial DNA (mtDNA) were analyzed in a sample of 137 unrelated Japanese individuals living in Gifu Prefecture (central region of Japan) using polymerase chain reaction amplification and direct sequencing. Eighty-two different haplotypes resulting from 81 variable sites were found in the mtDNA HV1 region between positions 16061 and 16450. The most frequent haplotype (16223T, 16362C) was shared by ten individuals. The genetic diversity and the genetic identity were 0.985 and 0.022, respectively. The C-stretch region located around position 16189 was observed in 23.4% of this population sample. Sequence heteroplasmy at the position 16103 (A/G) was found in one individual.

DNA Fingerprinting↗
PubMedDate not supplied

Quantitative analysis of amplifiable DNA in tissues exposed to various environments using competitive PCR assays.

Competitive PCR assays were established for the mitochondrial DNA hypervariable region I and the human amelogenin locus. Using these assays, the copy numbers of DNA participating in PCR (amplifiable DNA) were quantified in tissues exposed to different environments. Human ribs, skin and nails were left in three exposure conditions (in the open air, in soil and in water). The amounts of amplifiable DNA in these tissues were quantified during a time period of up to two months. The amount of amplifiable DNA was well preserved in hard tissues (ribs and nails) regardless of the exposure conditions, whereas the soft tissues immersed in water showed a rapid decrease in amplifiable DNA. Strong PCR inhibition was observed in the DNA extracts obtained from buried bones. This phenomenon was clearly identified from an amplification failure of the internal standards in the competitive PCR. A preliminary examination to identify the PCR inhibitor suggested that the soil itself contributed to the inhibition. In addition, the amounts of amplifiable DNA in case samples were also investigated.

DNA↗
PubMed2001

Dynamics of serum hepatitis C virus load and quasispecies complexity during antiviral therapy in patients with chronic hepatitis C.

BACKGROUND: Hepatitis C virus (HCV) infection is a dynamic process during which viral genetic variants continuously develop as a result of the virus adaptation to the host's immune system. The level of viremia and the complexity of the hypervariable region 1 (HVR 1) quasispecies of hepatitis C virus during antiviral therapy reflect the dynamic balance between the viral and host components in response to therapy. OBJECTIVE: The aim of the study was to evaluate the dynamics of HCV viremia and the complexity of the HVR 1 quasispecies during the induction phase of a triple combination therapy regimen in nonresponders to earlier anti-HCV treatment. STUDY DESIGN: Ten patients with chronic hepatitis C undergoing antiviral combination therapy with interferon-alpha, ribavirin, and amantadine were studied. The serum HCV RNA level was monitored by a quantitative RT-PCR assay up to 3 months after start of treatment. The HVR 1 quasispecies complexity was analysed by an "in house" nested RT-PCR mediated single-strand conformation polymorphism (SSCP) assay. RESULTS: Baseline serum HCV RNA levels ranged from 1.94x10(6) to 5.53x10(6) copies/ml. In all patients, HCV subtype 1b was found. At the start of therapy, the SSCP assay revealed a high complexity pattern (at least six SSCP bands) in all patients. None of the patients responded within 4 weeks of treatment, however, the serum HCV RNA level decreased by one to two logs in eight patients. At week 4 after start of treatment, there was a decrease of SSCP bands in five patients. In four patients, SSCP bands remained unchanged and in one patient SSCP bands increased. At month 3 after start of treatment, serum HCV RNA was not detectable in one patient. CONCLUSION: Because of the low number of patients involved in this study, prediction of therapeutical success based on the quasispecies complexity was not possible. Larger studies are urgently needed.

Adult↗
PubMed2001

Single domain camel antibodies: current status.

The antigen-binding capacity of the paired variable domains of an antibody is well established. The observation that the isolated heavy chains of anti-hapten antibodies retain some antigen-binding capacity in the absence of light chains led to attempts to obtain an even smaller antigen-binding unit in a VH format. Unfortunately, the poor solubility, the reduced affinity for the antigen and the irreproducible outcome showed that additional protein engineering would be required to successfully generate single-domain antibody fragments. By serendipity, it was discovered that this engineering is already performed continuously in nature. Part of the humoral immune response of camels and llamas is based largely on heavy-chain antibodies where the light chain is totally absent. These unique antibody isotypes interact with the antigen by virtue of only one single variable domain, referred to as VHH. Despite the absence of the VH-VL combinatorial diversity, these heavy-chain antibodies exhibit a broad antigen-binding repertoire by enlarging their hypervariable regions. Methods are described to tap the VHH repertoire of an immunised dromedary or llama. These VHH libraries contain a high titre of intact antigen-specific binders that were matured in vivo. Synthetic libraries of a 'camelised' human VH, a mouse VH or a camelid VHH scaffold with a randomised CDR3 could constitute a valid alternative to immune libraries to retrieve useful single-domain antigen binders. The recombinant VHH that are selected from such libraries are well expressed, highly soluble in aqueous environments and very robust. Some in vivo matured VHH were also shown to be potent enzyme inhibitors, and the low complexity of the antigen-binding site is an asset in the design of peptide mimetics. Because of their smaller size and the above properties, the VHH clearly offer added-value over conventional antibody fragments. They are expected to open perspectives as enzyme inhibitors and intrabodies, as modular building units for multivalent or multifunctional constructs, or as immuno-adsorbents and detection units in biosensors.

Amino Acid Sequence↗
PubMed1997

Discrimination of single-nucleotide polymorphisms in human DNA using peptide nucleic acid probes detected by MALDI-TOF mass spectrometry.

Human genomic and mitochondrial DNA contain large numbers of single-nucleotide polymorphisms (SNPs), many of which are linked to known diseases. Rapid and accurate genetic screening for important SNPs requires a general methodology which is easily implemented. We present here an approach to SNP discrimination based on high-specificity hybridization of peptide nucleic acid (PNA) probes to PCR-amplified DNA. The assay is directly applied to polymorphisms located within hypervariable region 1 of the human mitochondrial genome and type 1 suballeles of the human leukocyte antigen DQ alpha gene. Captured, single-stranded DNA molecules prepared by PCR amplification are hybridized with PNA probes in an allele-specific fashion. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is then used for rapid, precise, and unambiguous detection and identification of the hybridized PNA probes. Since PNA oligomers bind strongly to complementary DNA under minimal salt conditions, the use of PNA probes is compatible with MALDI-TOFMS. The unparalleled ability of MALDI-TOFMS analysis in terms of molecular weight resolution and accuracy, in conjunction with the highly specific PNA hybridization afforded by this method, offers promise for development into a multiplexed, high-throughput screening technique.

DNA↗
PubMed1993

Phage display and selection of a site-directed randomized single-chain antibody Fv fragment for its affinity improvement.

The affinity of an antibody Fv fragment was improved by semirational design involving site-directed randomization and phage display. On the basis of the predicted model of an anti-2-phenyloxazol-5-one (phOx) antibody Fv fragment, into which the ligand was inserted with the help of nuclear Overhauser enhancement (NOE) data, residues close to the hapten were identified. Seven of these residues in the third hypervariable regions of light and heavy chains were randomized in polymerase chain reactions (PCR) using degenerate oligonucleotides. Resulting clones were expressed as single-chain Fv (scFV) fragments on the surface of filamentous phage and selected for binding to phOx-conjugated bovine serum albumin. Selected Fv fragments were analyzed for hapten affinity by fluorescence quenching, and several mutants with improved affinities were identified. Phage selection on the basis of binding was very successful when phage scFv mutants differed in affinity by at least a factor of 6. Smaller differences did not result in predominant selection of the best binder. Combination of the two point mutations most crucial for improved hapten binding decreased the dissociation constant of the Fv for phOx 11-14-fold. Hapten binding of the improved Fv was analyzed in NOE experiments.

Amino Acid Sequence↗
PubMed1992

Dynamical structure of the antibody combining site as studied by 1H-15N shift correlation NMR spectroscopy.

The Fv fragment, which is a smallest antigen-binding unit of immunoglobulin, has been used for a 1H-15N shift correlation NMR study of the dynamical structure of the antibody combining site. Fv has been prepared by clostripain digestion of a mouse anti-dansyl IgG2a monoclonal antibody that lacks the entire CH1 domain. We have previously reported that of the six hypervariable regions, three each from the heavy chain (H1, H2, and H3) and the light chain (L1, L2, and L3), H3 is primarily responsible for the antigen binding in the anti-dansyl Fv fragment. The backbone amide nitrogens of all non-proline amino acid residues in H3 have been multiply labeled with 15N. [15N]T2 relaxation times and hydrogen-deuterium exchange rates of the amide groups of the main chain were measured in the absence and presence of epsilon-dansyl-L-lysine (DNS-Lys). It has been shown that (1) in the absence of DNS-Lys H3 displays a significant degree of internal motion and (2) antigen binding induces a significant change in the dynamical structure of H3.

Amino Acid Sequence↗
PubMed1992

Isotope-edited nuclear magnetic resonance study of Fv fragment of anti-dansyl mouse monoclonal antibody: recognition of the dansyl hapten.

An isotope-edited proton nuclear magnetic resonance study is reported of Fv, which is the smallest antigen recognition unit composed of VH and VL domains. Fv has been obtained by clostripain digestion of a short-chain anti-dansyl mouse IgG2a monoclonal antibody [Igarashi, T., Sato, M., Katsube, Y., Takio, K., Tanaka, T., Nakanishi, M., & Arata, Y. (1990) Biochemistry 29, 5727-5733]. A variety of stable-isotope-labeled anti-dansyl Fv analogues have been prepared. The aromatic proton resonances for all Tyr residues of the Fv fragment have been assigned in the absence and presence of epsilon-dansyl-L-lysine by means of isotope-edited homonuclear and heteronuclear two-dimensional NMR experiments. On the basis of the established assignments, it has been concluded that the dansyl ring is bound through Tyr-96H and Tyr-104H to both ends of H3, the third hypervariable region of the heavy chain. We also suggest that the antigen binding results in the formation of a hydrophobic core comprising the dansyl ring and the aromatic rings of Tyr-96H and Tyr-104H.

Animals↗